Lonelygirl15

No one else has attempted this so I am going to try to help in this matter. This first part is a bit of info you need to understand so that you can help Bree. So just bear with me while we go ever all the technical stuff….I’ll try to make it as brief and painless as I can.

OK DB, Here is the deal:

Ribozymes are actually catalytic RNA molecules and they have several subclasses. Ribozymes have the ability to cut or change the length of existing RNA molecules( and some proteins but I won’t get into that because I do not think that would be helpful considering the little amount of info that we do know about WHY Bree is testing as trait positive); Ribozymes can have the ability to cut themselves or other RNA molecules( a process called splicing), but this ability depends on the function/molecular arrangement of the RNA molecule being acted upon and/or the ribozyme itself. Typically, Ribozymes are not stable molecules….which is why they have the ability to catalyze changes in RNA in the way that they do…..Which is also why the body cannot readily use them or rely on them for chemical signaling throughout the cell.

All RNA is actually manufactured from DNA in a process called transcription which occurs inside the nucleus of a cell. Transcription occurs when a gene or multiple genes in the DNA strand are used as a template to construct a pre-RNA molecule(strand). Subsequently, the pre-RNA molecule will then be identified as its specific type(based on what gene it originated from) so that it an be modified to perfom its specific functionality. The most typical forms of RNA are tRNA, mRNA( aka pre-mRNA after its been modified), and rRNA. Ribozymes and mRNA are actually formed after transcription before the RNA strands have left the nucleus and entered the cytosol. The process of forming mRNA and ribozymes is actually a modification step called post-transcriptional processing.

The post transcriptional processing converts pre-mRNA into mRNA and can also form ribozymes. However, Ribozymes themselves can also be transcribed directly from the DNA template, this just depends on the type of ribozyme and its functionality. During Post transciptional modification in the human body, ribozymes are often used to facilitate a process called “splicing” . To initiate “splicing” the ribozymes will actually assimilate themselves into small groups and associate themselves with proteins to form small complexes called ‘spliceosomes’. The spliceosomes will then situate themselves along the pre-mRNA strand and start to excise specifically targeted pieces of the pre-mRNA, called introns, from the pre-mRNA strand. The removal of the introns form the pre-mRNA strand allows for the formation of a few more ribozymes and allows the cell to specify the exact chain of nucleotide sequences that will be formed into the mRNA and therefore, specify its resultant products as well.

The most important thing to remember about RNA and ribozymes is that they are actually only an intermediary step between transcription and translation.—translation is defined below.

Translation occurs when mRNA (the already processed pre-mRNA nucleotide sequence) is ( with the help of tRNA and rRNA) translated into an amino acid sequence that will ultimately result in the formation of a protein. Translation is important because most proteins are very stable and can be used for a variety of chemical process throughout the cell.

Ok..so now you are probably asking yourself why I just gave you a lecture on molecular biology….hang in there I have a point…I promise!

First lets review both process of translation and transcription to see how the are put together.


Transcription:

DNA(goes through transcription)--> pre-mRNA, tRNA, rRNA



Post transcriptional Processing ( only the pertinent parts):


Pre-mRNA + ribozymes (nucleotides added/removed/modified and introns removed) --> mRNA and newly made Ribozymes



Translation:

{mRNA + tRNA + rRNA + individual amino acids}(goes through translation) --> Protiens


So…now we see the dilemma!

IF Bree is actually trait positive because of the increased quantity of ribozymes that she has in compariosn to the rest of the population (as Daniel has suggested), then we first have to figure out which specific genes are being transcripted into the pre-mRNA that are producing the large amounts of ribozymes. Once those are identified then we maybe able to find a way to inhibit those specific ribozymes…….but that could also be dangerous because anything that we might use to inhibit one specific kind of ribozyme could potentially inhibit many others because most ribozymes will have similar chemical properties….and…Bree needs her ribozymes. Lol…….there might also be a way to just suppress the quantity of ribozymes but I think that would be more difficult.

However, I think the solution to making bree trait negative might be much more simple than trying to chemically inhibit Bree’s ribozymes.

We know that bree’s father was investigating ribozymes….and based on the few glimpses we got of the research notebook…. it looked as if he were investigating more than one kind…..
What if Bree is trait positive because one of her genes that codes for one ( or some) of her ribozymes is actually different than the majority of the population, i.e. one of here genes has mutated?

Since we know that most ribozymes facilitate the extraction of nucleotides that ‘aren’t supposed” to be in the finished product of an mRNA strand…..that means that there is a very good possibility that the protein produced after translation ( in Bree’s body) would be a completely different protein than that of the rest of the population. If that were the case, then the only thing that we would have to identify would be the types of proteins in Bree’s body….which could be done easily by taking a tissue sample and testing it via electrophoresis……and then compare her proteins to that of the general population. Once you are able to identify the protein there are several ways to inhibit the protein production or its appearance in the blood stream....


But I think I am getting ahead of myself right now…

My point is…….. based on how little information we know about why Bree is testing as trait positive and the information that we know about how ribozymes work….I think that the first logical step of action here is to find out what they actually test for when they test for the “trait”. If you can not find out what it is the HoO is testing for, it would be beneficial to know what kind of test they actually were running and if they are using a chemical reagent, you would need to know what the reagent is so that you could research the kinds of substances that would react with that specific reagent to provide positive or negative results…….


Ok I think that is enough from me right now you have enough to chew on for a while….. Good luck!

~~FLY

Wow!!! Great research Fly!!! I really think you are on to something here! You amaze me And you said everything in a way that I actually understood. Props to you for that! You are awesome!!!!

This is a great post. I hope you're listening, Daniel!

Thanks for the positive feed back....but it wasn't exactly research...I'm a biology and chemistry major, so I kinda have to know these things

i hope I explained it thoroughly enough...the concepts are slightly abstract so it makes it hard to communicate exactly how everything works. lol

If you guys have any questions just let me know.

so, would the ceremony [assuming it involves these ribozymes] harm Bree? or would they just extract the extra ones and then move one and leave her alone? would they come back for more? i don't know if you can answer this, but thought i'd ask. :]

thanks in advance, chica!

Actually, it would be difficult to extract the ribozymes themselves because they are so volatile. It is more likey that the HoO are searching for the end product --proteins.

However, if it is infact the riboszymes they are after...then it would not be extremely dangerous if they were able to extract them from her in some way.

When a cell senses that the quantity of a specific ribozyme is below its normal levels, a process of checmical reactions inside the cell would trigger the production of more ribozymes via transcription......so...as long as a cells had enough time to repopulated the ribozymes that had decreased before the next extraction...there would really be no harm to Bree...except...that...it could potentially be painful...ribozymes are not normally let outside of the cell wall or into the blood stream....so that means the HoO would have to get live tissue samples....ewwww

It could very well be the HoO's intention to harvest her ribozymes...But if that was the case...why wouldn't they just make them? The technology is avalible to do so.....and many reports have shown repeated success in producing synthetic ribozymes that function properly.


ummm...did I answer that? lol let me know.


;p
~~FLY

flychiqk wrote:It could very well be the HoO's intention to harvest her ribozymes...But if that was the case...why wouldn't they just make them? The technology is avalible to do so.....and many reports have shown repeated success in producing synthetic ribozymes that function properly.

They might want them straight from a young, pure little Hymn of Oner.

LMBO...that is true....they are a cult....who knows why they are doing what they are doing.....there might not even be any scientific fact to base their actions on....it might just be some kinda of crazy cult thing.....creepy!

Ahh but Daniel might understand better after watching this explanation:

http://www.youtube.com/watch?v=u9dhO0iCLww

AWESOME summary and analysis.

Long explanation short, find a way to fool their testing methods. Like faking a drug test by using clean urine from another donor. But there's a twist, you don't whether bree is trustworthy at the moment. This is just a mite harder than faking a drug test, considering your dealing with sub cellular components rather than straight up chemicals which are more easily neutralized. So unless your a biochemist like our friend flychiqk your gonna be having some fun chasing down a safe method to neutralize the orders tests, without bree knowing outright. In other words be shifty don't tell bree anything, and share more info with us.

Edit: once you've fooled the order run like an Olympian. They may just kill bree and you guys if your no longer worth anything to them.

Long explanation short, find a way to fool their testing methods. Like faking a drug test by using clean urine from another donor. But there's a twist, you don't whether bree is trustworthy at the moment. This is just a mite harder than faking a drug test, considering your dealing with sub cellular components rather than straight up chemicals which are more easily neutralized. So unless your a biochemist like our friend flychiqk your gonna be having some fun chasing down a safe method to neutralize the orders tests, without bree knowing outright. In other words be shifty don't tell bree anything, and share more info with us.

Actually, there are several ways in which we would stop the expression of either the rusultant protien, or inhibit the expression of the ribozyme itself. Its not as simple as swapping urine, but a few of the ways are safe....but there is no way to know what to do until we can find out how they test for the "trait" and what they are testing for.

~FLY

flychiqk wrote:Actually, there are several ways in which we would stop the expression of either the rusultant protien, or inhibit the expression of the ribozyme itself. Its not as simple as swapping urine, but a few of the ways are safe....but there is no way to know what to do until we can find out how they test for the "trait" and what they are testing for.

~FLY

True, I think the key is in that book. It probably clearly identifies what we're looking for, though db probably doesn't know what to look for, that's why he should share more info with us.

Oxdeltaxo wrote:


True, I think they key is in that book. It probably clearly identifies what we're looking for, though db probably doesn't know what to look for, that why he should share more info with us.

DID YOU HEAR THAT DANIEL? WE NEED MORE INFO!!!!!!!!!!!!!!

When you can please...I know you have your hand full...

*snickers*

I think we also need to think about what the Order could want with either ribozymes or unique proteins. Are they trying to stop death? Treat diseases? Some other wacky completely nonplausible culty claim based on pop pseudo science?

I hate to say this, but if they just want Bree's DNA (and therefore the coding sequence to create the ribozymes and/or proteins synthetically), can't they just take a sample? What is all this "ceremony" garbage about? Is it like kosher meat--their religion requires it be taken a certain way, but in the end it's still just meat"?

Ok, I've whipped out the good ol' molecular bio book. From
Molecular Biology of the Gene by J. Watson et al:

It was widely believed for many years that only proteins could be enzymes. An enzyme must be able to bind a substrate, carry out a chemical reactions, release this product, and repeat this sequence of events many times. Proteins are well-suited to this task because they are composed of many different kinds of amino acids and they can fold into complex tertiary structures with binding pockets for the substrate and small molecule co-factors and an active site for catalysis. now we know that RNAs, which as we have seen can similarly adopt complex tertiary structures, can also be biological catalysts. Such RNA enzymes are known as ribozymes, and they exhibit many of the features of a classic enzyme, such as an active site, a binding site for a substrate, and a binding site for a co-factor, such as a metal ion.
One of the first ribozymes to be discovered was RNAse P, a ribonuclease that is involved in generating tRNA molecules from larger, precursor RNAs. RNAse P is composed of both RNA and protein; however, the RNA moiety alone is the catalyst. The protein moiety of RNAse P facilitates the reaction by shielding the negative charges on the RNA so that it can bind effectively to its negatively-charged substrate. The RNA moiety is able to catalyze cleavage of the tRNA precursor in the absence of the protein if a small, postively charged counter ion, such as the peptide spermidine, is used to shield the repulsive, negative charges. Other ribozymes carry out trans-esterfication reactions involved in the removal of intervening sequences known as introns from precursors to certains mRNAs, tRNAs, and ribosomal RNAs in a process known as RNA splicing.

RNA splicing is what flychiqk was describing above.